MRHMMs 2 – Multivariate Regression Hidden Markov Models and the variantS

MRHMMs 2

:: DESCRIPTION

MRHMMs accommodates a variety of HMMs that can be flexibly applied to many biological studies and beyond.

::DEVELOPER

MRHMMs team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/ WIndows
  • C Compiler

:: DOWNLOAD

 MRHMMs

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Feb 27. [Epub ahead of print]
MRHMMs: Multivariate Regression Hidden Markov Models and the variantS.
Lee Y1, Ghosh D, Hardison RC, Zhang Y.

MiRKAT 1.2.1 – Microbiome Regression-Based Analysis Tests

MiRKAT 1.2.1

:: DESCRIPTION

MiRKAT is a package for testing microbiome and outcome association, adjusting for possible covariates.

::DEVELOPER

Hongzhe Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

MiRKAT

:: MORE INFORMATION

Citation

Wilson N, Zhao N, Zhan X, Koh H, Fu W, Chen J, Li H, Wu MC, Plantinga AM.
MiRKAT: kernel machine regression-based global association tests for the microbiome.
Bioinformatics. 2021 Jul 12;37(11):1595-1597. doi: 10.1093/bioinformatics/btaa951. PMID: 33225342; PMCID: PMC8495888.

SIMreg 1.32 – Gene-trait Similarity Regression for Marker-set Association Analysis

SIMreg 1.32

:: DESCRIPTION

SIMreg is a tool to perform maker-set association analysis. Association analysis at gene, pathway, or exon levels (here by marker-set analysis) hold great promise in evaluating modest etiological effects of genes with GWAS or sequence data.

::DEVELOPER

Jung-Ying Tzeng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/Linux
  • R

:: DOWNLOAD

 SIMreg

 :: MORE INFORMATION

Citation

Am J Hum Genet. 2011 Aug 12;89(2):277-88. doi: 10.1016/j.ajhg.2011.07.007.
Studying gene and gene-environment effects of uncommon and common variants on continuous traits: a marker-set approach using gene-trait similarity regression.
Tzeng JY1, Zhang D, Pongpanich M, Smith C, McCarthy MI, Sale MM, Worrall BB, Hsu FC, Thomas DC, Sullivan PF.

POME – Possion Mixed-Effects Regression for RNA-seq Data

POME

:: DESCRIPTION

POME (Poisson mixed-effects model) implement a novel method specifically designed for quantifying exon-level gene expression in RNA-Seq.

::DEVELOPER

Michael Yu Zhu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 POME

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jan 1;28(1):63-8. doi: 10.1093/bioinformatics/btr616. Epub 2011 Nov 8.
Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq.
Hu M, Zhu Y, Taylor JM, Liu JS, Qin ZS.

BLR 1.6 / BGLR 1.0.8 – Bayesian Linear Regression

BLR 1.6 / BGLR 1.0.8

:: DESCRIPTION

BLR (Bayesian Linear Regression) was designed to fit parametric regression models using different types of shrinkage methods. Linear regression with high-dimensional predictors (e.g. SNP) and pedigree.

BGLR: Bayesian Generalized Linear Regression

::DEVELOPER

Paulino Perez Rodriguez <perpdgo at colpos.mx>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BLR / BGLR

:: MORE INFORMATION

Citation:

Gustavo de los Campos, Hugo Naya , Daniel Gianola , José Crossa , Andrés Legarra , Eduardo Manfredi , Kent Weigel and José Miguel Cotes
Predicting Quantitative Traits With Regression Models for Dense Molecular Markers and Pedigree.
Genetics. 182;375-385, 2009. (doi:10.1534/genetics.109.101501)

rrBLUP 4.6.1 – Ridge Regression and other kernels for Genomic Selection

rrBLUP 4.6.1

:: DESCRIPTION

rrBLUP is an R package for genomic selection and association mapping.

::DEVELOPER

Endelman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

 rrBLUP

:: MORE INFORMATION

Citation

Jeffrey B. Endelman
Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP
The Plant Genome Vol. 4 No. 3, p. 250-255 doi:10.3835/plantgenome2011.08.0024

IsoLasso 2.6.1 – A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly

IsoLasso 2.6.1

:: DESCRIPTION

IsoLasso is an algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.

::DEVELOPER

Wei Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MatLab
  • C Compiler

:: DOWNLOAD

  IsoLasso

:: MORE INFORMATION

Citation

J Comput Biol. 2011 Nov;18(11):1693-707. doi: 10.1089/cmb.2011.0171. Epub 2011 Sep 27. IsoLasso: a LASSO regression approach to RNA-Seq based transcriptome assembly. Li W1, Feng J, Jiang T.

copynumber 1.32.0 – Segmentation of Single- and multi-track Copy Number data by penalized least Squares Regression

copynumber 1.32.0

:: DESCRIPTION
The R package copynumber is a software suite for segmentation of single- and multi-track copy number data using algorithms based on coherent least squares principles.

::DEVELOPER

Research Group for Biomedical Informatics (BMI)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R / BioCOnductor

:: DOWNLOAD

 copynumber

:: MORE INFORMATION

Citation:

BMC Genomics. 2012 Nov 4;13:591. doi: 10.1186/1471-2164-13-591.
Copynumber: Efficient algorithms for single- and multi-track copy number segmentation.
Nilsen G1, Liestøl K, Van Loo P, Moen Vollan HK, Eide MB, Rueda OM, Chin SF, Russell R, Baumbusch LO, Caldas C, Børresen-Dale AL, Lingjaerde OC.

RAPID – Regression-based Accurate Prediction of protein Intrinsic Disorder Content

RAPID

:: DESCRIPTION

RAPID is a server providing fast and accurate sequence based prediction of protein disorder content.

::DEVELOPER

Kurgan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Biochim Biophys Acta. 2013 Aug;1834(8):1671-80. doi: 10.1016/j.bbapap.2013.05.022. Epub 2013 Jun 1.
RAPID: fast and accurate sequence-based prediction of intrinsic disorder content on proteomic scale.
Yan J1, Mizianty MJ, Filipow PL, Uversky VN, Kurgan L.

LogMiNeR 0.1.0 – Logistic Multiple Network-constrained Regression

LogMiNeR 0.1.0

:: DESCRIPTION

LogMiNeR is a method for analyzing high-throughput transcriptional profiling data (e.g., microarray or RNA-seq) in which multiple networks encoding prior knowledge are incorporated within a logistic modeling framework to improve model interpretability.

::DEVELOPER

Kleinstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

LogMiNeR

:: MORE INFORMATION

Citation

Avey S, et al.
Multiple network-constrained regressions expand insights into influenza vaccination responses.
Bioinformatics,33 (14), i208-i216 2017 Jul 15